AMBER Archive (2002)

Subject: Re: About heating...

From: David A. Case (case_at_scripps.edu)
Date: Wed Dec 18 2002 - 13:42:51 CST

On Wed, Dec 18, 2002, Andrei Leitão wrote:

> I am doing a molecular modeling study (500ps) to a DNA
> decamer including explicit solvent molecules (H2O) and
> counterions (Na+) at constant pressure.
>
> I made a molecular dynamic at 300K without this heating
> procedure and one of the end base pairs was very distorted
> from the axis.

Take a look at the equilibration procedure in the DNA tutorial on the
Amber web site. Two comments on your system:

(a) don't use constant pressure until the system is already heated up
at constant volume;

(b) generally, one should heat and equilibrate with constraints to the
initial structure (set ntr=1); after that is done, you can remove the
constraints.

In spite of all of this, it is not unusual (or necessarily wrong) to see
an end base-pair distorted from the axis (although I don't know what you
really mean by "very distorted"...)

..good luck...dac 

-- 

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